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- JP2010501179A5 JP2010501179A5 JP2009525579A JP2009525579A JP2010501179A5 JP 2010501179 A5 JP2010501179 A5 JP 2010501179A5 JP 2009525579 A JP2009525579 A JP 2009525579A JP 2009525579 A JP2009525579 A JP 2009525579A JP 2010501179 A5 JP2010501179 A5 JP 2010501179A5
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- 241000318927 Shrimp white spot syndrome virus Species 0.000 claims description 60
- 239000000523 sample Substances 0.000 claims description 38
- 150000007523 nucleic acids Chemical class 0.000 claims description 31
- 108020004707 nucleic acids Proteins 0.000 claims description 29
- 230000000295 complement Effects 0.000 claims description 19
- 230000003321 amplification Effects 0.000 claims description 12
- 229920003013 deoxyribonucleic acid Polymers 0.000 claims description 12
- 238000003199 nucleic acid amplification method Methods 0.000 claims description 12
- 239000003795 chemical substances by application Substances 0.000 claims description 8
- 238000000034 method Methods 0.000 claims description 4
- 238000005382 thermal cycling Methods 0.000 claims description 4
- 238000006243 chemical reaction Methods 0.000 claims description 2
- 230000037030 denaturation temperature Effects 0.000 claims description 2
- 238000003745 diagnosis Methods 0.000 claims description 2
- 238000009396 hybridization Methods 0.000 claims description 2
- 239000012086 standard solution Substances 0.000 claims description 2
- 229920002287 Amplicon Polymers 0.000 description 2
- OFEZSBMBBKLLBJ-BAJZRUMYSA-N CORDYCEPIN Chemical group C1=NC=2C(N)=NC=NC=2N1[C@@H]1O[C@H](CO)C[C@H]1O OFEZSBMBBKLLBJ-BAJZRUMYSA-N 0.000 description 2
- 239000003153 chemical reaction reagent Substances 0.000 description 2
- 230000002401 inhibitory effect Effects 0.000 description 2
- 239000000203 mixture Substances 0.000 description 2
- 239000000126 substance Substances 0.000 description 2
- 231100000277 DNA damage Toxicity 0.000 description 1
- 241000238557 Decapoda Species 0.000 description 1
- 229920001850 Nucleic acid sequence Polymers 0.000 description 1
- 230000015572 biosynthetic process Effects 0.000 description 1
- 230000001809 detectable Effects 0.000 description 1
- 238000001514 detection method Methods 0.000 description 1
- 239000005546 dideoxynucleotide Substances 0.000 description 1
- 238000011156 evaluation Methods 0.000 description 1
- 238000001917 fluorescence detection Methods 0.000 description 1
- 238000005755 formation reaction Methods 0.000 description 1
- 230000002779 inactivation Effects 0.000 description 1
- 239000002777 nucleoside Substances 0.000 description 1
- 125000003835 nucleoside group Chemical group 0.000 description 1
- 125000002467 phosphate group Chemical group [H]OP(=O)(O[H])O[*] 0.000 description 1
- 238000003752 polymerase chain reaction Methods 0.000 description 1
- 239000001226 triphosphate Substances 0.000 description 1
- 235000011178 triphosphate Nutrition 0.000 description 1
- 125000002264 triphosphate group Chemical class [H]OP(=O)(O[H])OP(=O)(O[H])OP(=O)(O[H])O* 0.000 description 1
Description
表7に要約される結果は、然るべきWSSV鋳型が存在するとき、各プライマー/プローブセットについて然るべきサイズのアンプリコン産物が産生されたことを実証している。鋳型の最小検出レベルは、使用されるプライマー及びプローブに応じて100〜1000コピー/rxnであった。鋳型を含まない試料は、検出可能な産物を産生しなかった。
増幅(CT)及びアンプリコン産物の形成は、鋳型の出発濃度の対数にそれぞれ反比例及び正比例した。
The results summarized in Table 7 demonstrate that the appropriate size amplicon product was produced for each primer / probe set when the appropriate WSSV template was present. The minimum detection level of template was 100-1000 copies / rxn depending on the primer and probe used. Samples containing no template produced no detectable product.
Amplification (CT) and amplicon product formation were inversely and directly proportional to the log of the starting template concentration, respectively.
以上、本発明を要約すると、下記のとおりである。
1.配列番号1に記載の単離されたWSSV診断用プライマー配列又は配列番号1と完全に相補的な単離核酸分子。
2.配列番号2に記載の単離されたWSSV診断用プライマー配列又は配列番号2と完全に相補的な単離核酸分子。
3.配列番号3に記載の単離されたWSSV診断用プライマー配列又は配列番号3と完全に相補的な単離核酸分子。
4.配列番号4に記載の単離されたWSSV診断用プライマー配列又は配列番号4と完全に相補的な単離核酸分子。
5.配列番号5に記載の単離されたWSSV診断用プライマー配列又は配列番号5と完全に相補的な単離核酸分子。
6.配列番号6に記載の単離されたWSSV診断用プライマー配列又は配列番号6と完全に相補的な単離核酸分子。
7.配列番号7に記載の単離されたWSSV診断用プライマー配列又は配列番号7と完全に相補的な単離核酸分子。
8.配列番号8に記載の単離されたWSSV診断用プライマー配列又は配列番号8と完全に相補的な単離核酸分子。
9.WSSVゲノム内の核酸の領域を増幅する核酸増幅反応をプライムする能力を有する、上記1〜8のいずれかに記載の2つの異なるWSSV診断用プライマー配列の対。
10.配列番号1及び2、配列番号3及び4、配列番号5及び6、配列番号7及び8、配列番号3及び6、配列番号3及び配列番号5の完全相補体、並びに配列番号6及び配列番号4の完全相補体からなる群から選択される、上記9に記載の2つの異なるWSSV診断用プライマー配列の対。
11.上記9に記載のWSSV診断用プライマー配列の少なくとも1つの対を含むWSSVの検出用キット。
12.耐熱性ポリメラーゼ、4つの異なるデオキシヌクレオチド三リン酸の混合物、核酸結合性蛍光分子、試料内部対照プライマーの少なくとも1つの対、少なくとも1つの鋳型内部対照及び鋳型内部対照プライマーの少なくとも1つの対、並びにWSSV診断用プライマー配列の少なくとも1つの対により増幅可能なWSSVゲノム内の核酸の少なくとも1つの領域の一部分と相補的な配列を含むプローブからなる群から選択された少なくとも1つの試薬をさらに含む、上記11に記載のWSSVの検出用キット。
13.試料中のWSSVの存在を検出するための方法であって、
(i)WSSVを含むことが疑われる試料からDNAを提供する工程、及び
(ii)好適なハイブリダイゼーション条件下で、上記1〜8のいずれかに記載の単離されたWSSV診断用プライマー配列に由来するプローブにより上記DNAを探索する工程、
を含み、ハイブリダイズ可能な核酸断片が同定されると、それがWSSVの存在の確証となる、上記方法。
14.単離されたWSSV診断用プライマー配列に由来するプローブが、配列番号1、2、3、4、5、6、7、8、9、10、11、12、及びそれらの完全相補配列からなる群から選択される、上記13に記載の試料中のWSSVの存在を検出するための方法。
15.プローブが3’末端に複製阻害部分を含む、上記13に記載の方法。
16.複製阻害部分が、ジデオキシヌクレオチド、3’デオキシヌクレオチド、ミスマッチヌクレオシド又はヌクレオチドの配列、3’リン酸基及び化学剤からなる群から選択される、上記15に記載の方法。
17.3’デオキシヌクレオチドがコルジセピンである、上記16に記載の方法。
18.試料中のWSSVの存在を検出するための方法であって、
(i)WSSVを含むことが疑われる試料からDNAを提供する工程、及び
(ii)増幅産物が生成されるよう、上記9に記載のWSSV診断用プライマー配列の少なくとも1つの対により上記DNAを増幅する工程、
を含み、増幅産物が存在すると、それがWSSVの存在の確証となる上記方法。
19.(ii)の増幅工程がポリメラーゼ連鎖反応を用いて行われる、上記18に記載の試料中のWSSVの存在を検出するための方法。
20.(ii)の増幅工程が核酸結合性蛍光剤又は蛍光標識プローブの存在下で行われ、増幅産物の存在が蛍光検出を用いて確認される、上記18に記載の試料中のWSSVの存在を検出するための方法。
21.蛍光標識プローブが、配列番号17、18、及び19からなる群から選択される、上記20に記載の方法。
22.試料内部対照プライマーの少なくとも1つの対が(ii)の増幅工程に含まれることにより試料内部対照産物が産生される、上記18に記載の方法。
23.試料内部対照プライマーの少なくとも1つの対が、配列番号13、14及び配列番号15、16からなる群から選択される、上記22に記載の方法。
24.鋳型内部対照プライマーの少なくとも1つの対及び少なくとも1つの鋳型内部対照が、(ii)の増幅工程に含まれることにより鋳型内部対照産物が産生される、上記18に記載の方法。
25.試料中のWSSVの量を定量するための方法であって、
(i)WSSVを含むことが疑われる試料からDNAを提供する工程、
(ii)核酸結合性蛍光剤又は蛍光標識プローブの存在下での少なくとも変性温度と伸長温度との間の熱サイクリングによって、上記9に記載のWSSV診断用プライマー配列の少なくとも1つの対により上記DNAを増幅する工程、
(iii)上記熱サイクリング中に上記核酸結合性蛍光剤又は上記蛍光標識プローブによ
り生成される蛍光量を測定する工程、
(iv)上記核酸結合性蛍光剤又は上記蛍光標識プローブにより生成された蛍光量が基礎値を上回る固定閾値に達するときの閾値サイクル数を決定する工程、及び
(v)上記試料中のWSSVについて決定された上記閾値サイクル数を、既知の濃度の標準溶液を用いて決定された鋳型濃度の対数に対する閾値サイクル数の標準曲線と比較することにより、該試料中のWSSVの量を計算する工程、
を含む上記方法。
26.蛍光標識プローブが、配列番号17、18、及び19からなる群から選択される、上記25に記載の方法。
27.DNA損傷又はWSSV不活化の評価に用いられる、上記13、18、又は25のいずれかに記載の方法。
28.エビの健康及び発育を向上させるために化学的処置と組み合わせて用いられる、上記13、18、又は25のいずれかに記載の方法。
The present invention is summarized as follows.
1. An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 1 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 1.
2. An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 2 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 2.
3. An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 3 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 3.
4). An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 4 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 4.
5). An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 5 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 5.
6). An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 6 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 6.
7). An isolated WSSV diagnostic primer sequence as set forth in SEQ ID NO: 7 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 7.
8). An isolated WSSV diagnostic primer sequence set forth in SEQ ID NO: 8 or an isolated nucleic acid molecule that is completely complementary to SEQ ID NO: 8.
9. 9. Two different pairs of WSSV diagnostic primer sequences according to any of 1 to 8 above, having the ability to prime a nucleic acid amplification reaction that amplifies a region of nucleic acid within the WSSV genome.
10. SEQ ID NO: 1 and 2, SEQ ID NO: 3 and 4, SEQ ID NO: 5 and 6, SEQ ID NO: 7 and 8, SEQ ID NO: 3 and 6, the complete complement of SEQ ID NO: 3 and SEQ ID NO: 5, and SEQ ID NO: 6 and SEQ ID NO: 4 10. Two different pairs of WSSV diagnostic primer sequences according to claim 9, selected from the group consisting of:
11. 10. A kit for detecting WSSV comprising at least one pair of primer sequences for WSSV diagnosis according to 9 above.
12 Thermostable polymerase, mixture of four different deoxynucleotide triphosphates, nucleic acid binding fluorescent molecule, at least one pair of sample internal control primers, at least one template internal control and at least one pair of template internal control primers, and WSSV 11. The reagent of claim 11, further comprising at least one reagent selected from the group consisting of a probe comprising a sequence complementary to a portion of at least one region of nucleic acid within the WSSV genome that can be amplified by at least one pair of diagnostic primer sequences. The kit for detecting WSSV according to 1.
13. A method for detecting the presence of WSSV in a sample, comprising:
(I) a step of providing DNA from a sample suspected of containing WSSV; and (ii) an isolated WSSV diagnostic primer sequence according to any one of 1 to 8 described above under suitable hybridization conditions. Searching for the DNA with the probe derived from,
Wherein a hybridizable nucleic acid fragment is identified that confirms the presence of WSSV.
14 A group of probes derived from the isolated WSSV diagnostic primer sequence consisting of SEQ ID NOs: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, and their fully complementary sequences 14. A method for detecting the presence of WSSV in a sample as described in 13 above, selected from.
15. 14. The method of claim 13, wherein the probe comprises a replication inhibiting moiety at the 3 ′ end.
16. 16. The method of claim 15, wherein the replication inhibiting moiety is selected from the group consisting of dideoxynucleotides, 3 ′ deoxynucleotides, mismatched nucleosides or nucleotide sequences, 3 ′ phosphate groups and chemical agents.
17. The method according to 16 above, wherein the 3 ′ deoxynucleotide is cordycepin.
18. A method for detecting the presence of WSSV in a sample, comprising:
(I) providing DNA from a sample suspected of containing WSSV; and (ii) amplifying the DNA with at least one pair of WSSV diagnostic primer sequences as described in 9 above so that an amplification product is generated. The process of
Wherein the presence of amplification product is confirmation of the presence of WSSV.
19. 19. The method for detecting the presence of WSSV in a sample according to 18 above, wherein the amplification step of (ii) is performed using a polymerase chain reaction.
20. The presence of WSSV in the sample according to 18 above, wherein the amplification step (ii) is performed in the presence of a nucleic acid-binding fluorescent agent or a fluorescently labeled probe, and the presence of the amplification product is confirmed using fluorescence detection. How to do.
21. 21. The method of claim 20, wherein the fluorescently labeled probe is selected from the group consisting of SEQ ID NOs: 17, 18, and 19.
22. 19. The method of claim 18, wherein the sample internal control product is produced by including at least one pair of sample internal control primers in the amplification step of (ii).
23. 23. The method of claim 22, wherein at least one pair of sample internal control primers is selected from the group consisting of SEQ ID NOs: 13, 14 and SEQ ID NOs: 15, 16.
24. 19. The method of claim 18, wherein at least one pair of template internal control primers and at least one template internal control are included in the amplification step of (ii) to produce a template internal control product.
25. A method for quantifying the amount of WSSV in a sample, comprising:
(I) providing DNA from a sample suspected of containing WSSV;
(Ii) the DNA by at least one pair of WSSV diagnostic primer sequences described in 9 above by thermal cycling at least between the denaturation temperature and the extension temperature in the presence of a nucleic acid binding fluorescent agent or a fluorescently labeled probe. Amplifying process,
(Iii) measuring the amount of fluorescence generated by the nucleic acid-binding fluorescent agent or the fluorescently labeled probe during the thermal cycling;
(Iv) determining a threshold cycle number when the amount of fluorescence generated by the nucleic acid binding fluorescent agent or the fluorescent labeled probe reaches a fixed threshold value exceeding a basic value; and (v) determining the WSSV in the sample. Calculating the amount of WSSV in the sample by comparing the determined threshold cycle number to a standard curve of threshold cycle number versus logarithm of template concentration determined using a standard solution of known concentration;
Including the above method.
26. 26. The method of claim 25, wherein the fluorescently labeled probe is selected from the group consisting of SEQ ID NOs: 17, 18, and 19.
27. 26. The method according to any one of 13, 18, or 25, which is used for evaluation of DNA damage or WSSV inactivation.
28. 26. The method according to any one of 13, 18, or 25, wherein said method is used in combination with a chemical treatment to improve shrimp health and development.
Claims (13)
(i)WSSVを含むことが疑われる試料からDNAを提供する工程、及び
(ii)好適なハイブリダイゼーション条件下で、請求項1〜8のいずれか一項に記載の単離されたWSSV診断用プライマー配列に由来するプローブにより上記DNAを探索する工程、
を含み、ハイブリダイズ可能な核酸断片が同定されると、それがWSSVの存在の確証となる、上記方法。 A method for detecting the presence of WSSV in a sample, comprising:
(I) providing DNA from a sample suspected of containing WSSV, and (ii) for an isolated WSSV diagnostic according to any one of claims 1-8 under suitable hybridization conditions. Searching for the DNA with a probe derived from a primer sequence;
Wherein a hybridizable nucleic acid fragment is identified that confirms the presence of WSSV.
(i)WSSVを含むことが疑われる試料からDNAを提供する工程、及び
(ii)増幅産物が生成されるよう、請求項9に記載のWSSV診断用プライマー配列の少なくとも1つの対により上記DNAを増幅する工程、
を含み、増幅産物が存在すると、それがWSSVの存在の確証となる上記方法。 A method for detecting the presence of WSSV in a sample, comprising:
(I) providing DNA from a sample suspected of containing WSSV; and (ii) providing said DNA with at least one pair of WSSV diagnostic primer sequences according to claim 9 so that an amplification product is generated. Amplifying process,
Wherein the presence of amplification product is confirmation of the presence of WSSV.
(i)WSSVを含むことが疑われる試料からDNAを提供する工程、
(ii)核酸結合性蛍光剤又は蛍光標識プローブの存在下での少なくとも変性温度と伸長温度との間の熱サイクリングによって、請求項9に記載のWSSV診断用プライマー配列の少なくとも1つの対により上記DNAを増幅する工程、
(iii)上記熱サイクリング中に上記核酸結合性蛍光剤又は上記蛍光標識プローブによ
り生成される蛍光量を測定する工程、
(iv)上記核酸結合性蛍光剤又は上記蛍光標識プローブにより生成された蛍光量が基礎値を上回る固定閾値に達するときの閾値サイクル数を決定する工程、及び
(v)上記試料中のWSSVについて決定された上記閾値サイクル数を、既知の濃度の標準溶液を用いて決定された鋳型濃度の対数に対する閾値サイクル数の標準曲線と比較することにより、該試料中のWSSVの量を計算する工程、
を含む上記方法。 A method for quantifying the amount of WSSV in a sample, comprising:
(I) providing DNA from a sample suspected of containing WSSV;
(Ii) said DNA by at least one pair of WSSV diagnostic primer sequences according to claim 9 by thermal cycling at least between the denaturation temperature and the extension temperature in the presence of a nucleic acid binding fluorescent agent or a fluorescently labeled probe. Amplifying the process,
(Iii) measuring the amount of fluorescence generated by the nucleic acid-binding fluorescent agent or the fluorescently labeled probe during the thermal cycling;
(Iv) determining a threshold cycle number when the amount of fluorescence generated by the nucleic acid-binding fluorescent agent or the fluorescent labeled probe reaches a fixed threshold value exceeding a basic value; and (v) determining the WSSV in the sample. Calculating the amount of WSSV in the sample by comparing the determined threshold cycle number to a standard curve of threshold cycle number versus logarithm of template concentration determined using a standard solution of known concentration;
Including the above method.
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PCT/US2007/018345 WO2008024294A2 (en) | 2006-08-24 | 2007-08-17 | Sequences diagnostic for shrimp pathogens |
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US4683202A (en) * | 1985-03-28 | 1987-07-28 | Cetus Corporation | Process for amplifying nucleic acid sequences |
US5994056A (en) * | 1991-05-02 | 1999-11-30 | Roche Molecular Systems, Inc. | Homogeneous methods for nucleic acid amplification and detection |
US5824535A (en) * | 1996-01-17 | 1998-10-20 | Kou; Guang-Hsiung | Identification, purification and detection of WSBV (Baculovirus associated with white spot syndrome) |
CN1303942A (en) * | 1999-11-24 | 2001-07-18 | 国家海洋局第三海洋研究所 | Prawn white spot baculovirus genome DNA sequence and cDNA sequence |
US6872532B2 (en) * | 2002-05-20 | 2005-03-29 | Qgene Biotechnology, Inc. | Method and kit for detecting white spot syndrome virus |
US7429480B2 (en) * | 2005-01-10 | 2008-09-30 | National Taiwan University | Promoter sequences from WSSV immediate early genes and their uses in recombinant DNA techniques |
-
2007
- 2007-08-17 US US11/840,294 patent/US8057991B2/en not_active Expired - Fee Related
- 2007-08-17 BR BRPI0714643-4A2A patent/BRPI0714643A2/en not_active Application Discontinuation
- 2007-08-17 JP JP2009525579A patent/JP2010501179A/en active Pending
- 2007-08-17 CN CN2007800313979A patent/CN101522919B/en not_active Expired - Fee Related
- 2007-08-17 WO PCT/US2007/018345 patent/WO2008024294A2/en active Application Filing
-
2010
- 2010-03-01 HK HK10102153.7A patent/HK1137488A1/en not_active IP Right Cessation
-
2011
- 2011-09-21 US US13/238,451 patent/US8309301B2/en not_active Expired - Fee Related
- 2011-09-21 US US13/238,477 patent/US8293466B2/en not_active Expired - Fee Related
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